Week 10 Flashcards
3 types of RNA
T, M, R
Transcription steps (3)
- rna polymerase recruited at promoter with help of sigma factor
- rna polymerase synthesizes rna as bubble of unwound dna moves along
- at termination site both rna and rna polymerase are released, secondary structure, enzyme mediated
Proteins general functions (3)
catalytic proteins (enzymes)
structural proteins (parts of membranes, cell envelope, ribosomes)
regulatory proteins (dna binding, affecting transcription)
Primary structure
linear array of amino acids in a polypeptide, folds to form a more stable structure
protein composition
polymers of amino acids, both amino, carboxylic acid, linked to a-carbon
how are amino acids linked?
by polypeptide bonds through carboxyl carbon of one amino acid and amino nitrogen of a second
polypeptide
many amino acid links, proteins consist of 1+ polypeptides
amino acids, secondary structure
form hydrogen bonding (alpha helix or beta sheet)
amino acids, tertiary structure
three dimensional shape of a polypeptide from hydrophobic and other interactions
quaternary structure, amino acids
number and types of polypeptides that make a protein
denaturation
loss of structure and biological properties
transfer rnas
carry amino acids to translation machinery
anticodon
three bases that recognize codon (3 nucleic acids encoding an amino acid)
trna cognate (correct) amino acid brought together by aminoacyl-trna synthetases
general structure of trnas
single stranded
extensive secondary structure
contain bases modified post transcription
extensive double stranded regions formed by internal base pairing
cloverleaf shape
3’ end always had CCA added by CCA-adding enzyme instead of being encoded
Genetic code
a triplet of nucleic acid bases (codon) encoded a specific amino acid
64 possible codons
specific codons for starting and stopping translation
Degenerate code
multiple codons encode a singular amino acid (64 codons versus 22 natural amino acids) lacks one to one correspondence
Codon recognition occurs by:
specific base pairing with complementary anticodon sequence on trna
some trnas recog 1+
wobble
irregular base pairing allowed at third position of trna
codon bias
multiple codons for the same amino acid are not used equally
varies between organisms
correlated with trna concentration
start codon
translation begins with aug encoded n-formylmethionine in bacteria and methionine in archaea and eukarya
reading frame
triplet code required translation to begin at the correct nucleotide
RBS ensures proper reading frame in bacteria
stop (nonsense) codons
terminate translation (uaa, uag, uga) sometimes unusual amino acids selenocysteine and pyrrolysine can be encoded by stop codons
open reading frame
AUG followed by a number of codons and a stop codon
mechanisms of protein synthesis
3 steps, initiation, elongation, termination
mrna, trna, ribosomes
multiple proteins
needs GTP for energy
ribosomes
large complexes of proteins and rna where proteins are biosynthesized
polysomes
a complex formed by multiple ribosomes simultaneously translating a single mrna
release factors
recognize stop codon and cleave polypeptide from trna
dna binding proteins
bind to specific sites
different mechanisms
negative regulation, repression
inhibits gene expression, response to overabundance of an end product, mediated by repressor proteins. typically affects anabolic enzymes
negative regulation, induction
production of an enzyme in response to a signal or inducer, alleviates binding of repressor that blocks transcription, typically affects catabolic enzymes
positive regulation
activator binds to regulatory protein, directly activates transcription, binding sites on dna, improves recruitment and binding of rna pol to weak promoter
two component systems
prokaryotes regularly cellular metabolism in response to environmental fluctuations
1. ext signal transmitted directly to the target
2. ext signal detected by a sensor and then transmitted to regulatory machinery
sensor kinase
in cytoplasmic membrane, detects environmental signal and autophosphorylates
response regulator
in cytoplasm, dna binding protein that regulates transcription, also has feedback loop, terminates signal
quorum sensing
mechanism by which bacteria assess their population density
ensures sufficient # of cells present before initiating a response
autoinducers act as messengers to sense cell density
autoinducers
species specific molecules
diffuse freely across cell envelope
reach high concen inside cells only if many cells near
bone to specific activator proteins and trigger transcription of specific genes
chemotaxis
bacteria and archaea respond to challenges such as nutrient limitation and toxin accumulation by moving towards attractants and away from repellants
